Characterization of Microsatellite Primers in the Endangered Orchid Phaius australis and Cross‐Amplification to P. bernaysii (Orchidaceae)

Abstract

Premise of the study:The swamp orchid, Phaius australis (Orchidaceae), is nationally endangered due to illegal collection and habitat loss and fragmentation, resulting in a disjunct distribution in spring and coastal wetland ecotones along Australia’s east coast. Polymorphic microsatellite markers were developed to study genetic diversity and population structure for conservation and restoration purposes.Methods and Results:Illumina HiSeq high-throughput sequencing was used to develop 15 nuclear microsatellite markers, including 10 polymorphic markers for P. australis. Polymorphism at each marker was evaluated using 90 individuals from four natural populations. The number of alleles per locus ranged from one to three, and the observed and expected heterozygosity varied from 0.036 to 0.944 and from 0.035 to 0.611, respectively. These markers transferred successfully to congener P. bernaysii.Conclusions:The microsatellite markers will be useful for revealing levels of genetic diversity and gene flow for P. australis and may inform future conservation efforts.

Effects of human activities on the genetic characteristics of Phaius flavus populations

“…This is in contrast to other orchids such as Cypripedium macranthos (Pi = 0.154, Ho = 0.134, He = 0.153) [13], Geodorum eulophioides (Pi = 0.158, Ho = 0.012, He = 0.025) [18], and D. catenatum (Pi = 0.158, Ho = 0.099, He = 0.158) [29]. Similarly, P. avus from the BM population showed signi cant genetic diversity compared to congeneric Phaius such as P. australis and P. bernaysii [20]. Although G. eulophioides has a similar clonal growth pattern, a population with a high clone proportion (66.7%) results in lower genetic diversity [28].…”

“…Within the orchid family, SNPs have been used to elucidate phylogenetic relationships [17], evaluate genetic diversity [18], and detect genetic variations [19]. Scientists have developed microsatellite markers to examine the level of genetic diversity and gene ow in three species of Phaius [20]. However, these studies were unable to elucidate the genetic relationships among the three species.…”

“…avus in the Fujian Province was caused by anthropogenic disturbances [22]. Because of habitat fragmentation and illegal harvesting, the congener P. australis is listed as endangered in Australia [20]. In our study, the P. avus Beikengding Mount (BM) population was divided into two patches due to the construction of the Y013 village road from 2010 to 2012, which provided good material for examining the impact of human activities on the genetic characteristics of the population.…”

Microsatellite Dataset for Cultivar Discrimination in Spring Orchid (Cymbidium goeringii)

“…Microsatellites, also known as simple sequence repeats (SSRs), were first reported in C. goeringii by Moe et al [ 7 ], then several studies have examined microsatellite markers in molecular phylogenetic and horticultural studies of the genus Cymbidium [ 3 , 6 , 8 , 9 , 10 , 11 , 12 ] or the family Orchidaceae species [ 13 , 14 , 15 , 16 , 17 , 18 , 19 ]. In particular, Lee et al suggested the potential usefulness of microsatellite combined genotypes as a forensic authentication tool for discriminating among C. goeringii cultivars [ 3 ].…”

“…Microsatellites, also known as simple sequence repeats (SSRs), were first reported in C. goeringii by Moe et al [7], then several studies have examined microsatellite markers in molecular phylogenetic and horticultural studies of the genus Cymbidium [3,6,[8][9][10][11][12] or the family Orchidaceae species [13][14][15][16][17][18][19]. In particular, Lee et This study aimed to determine the cultivar-specific combined genotypes (CGs) of SSRs by analyzing multiple samples per cultivar in C. goeringii.…”